Epidemiology & Biostatistics Research Workshttp://hdl.handle.net/1903/7128
Sat, 19 Nov 2016 09:01:36 GMT2016-11-19T09:01:36ZLogic minimization and rule extraction for identification of functional sites in molecular sequenceshttp://hdl.handle.net/1903/13388
Logic minimization and rule extraction for identification of functional sites in molecular sequences
Cruz-Cano, Raul; Lee, Mei-Ling Ting; Leung, Ming-Ying
Background
Logic minimization is the application of algebraic axioms to a binary dataset with the purpose of reducing the number of digital variables and/or rules needed to express it. Although logic minimization techniques have been applied to bioinformatics datasets before, they have not been used in classification and rule discovery problems. In this paper, we propose a method based on logic minimization to extract predictive rules for two bioinformatics problems involving the identification of functional sites in molecular sequences: transcription factor binding sites (TFBS) in DNA and O-glycosylation sites in proteins. TFBS are important in various developmental processes and glycosylation is a posttranslational modification critical to protein functions.
Methods
In the present study, we first transformed the original biological dataset into a suitable binary form. Logic minimization was then applied to generate sets of simple rules to describe the transformed dataset. These rules were used to predict TFBS and O-glycosylation sites. The TFBS dataset is obtained from the TRANSFAC database, while the glycosylation dataset was compiled using information from OGLYCBASE and the Swiss-Prot Database.
We performed the same predictions using two standard classification techniques, Artificial Neural Networks (ANN) and Support Vector Machines (SVM), and used their sensitivities and positive predictive values as benchmarks for the performance of our proposed algorithm. SVM were also used to reduce the number of variables included in the logic minimization approach.
Results
For both TFBS and O-glycosylation sites, the prediction performance of the proposed logic minimization method was generally comparable and, in some cases, superior to the standard ANN and SVM classification methods with the advantage of providing intelligible rules to describe the datasets. In TFBS prediction, logic minimization produced a very small set of simple rules. In glycosylation site prediction, the rules produced were also interpretable and the most popular rules generated appeared to correlate well with recently reported hydrophilic/hydrophobic enhancement values of amino acids around possible O-glycosylation sites. Experiments with Self-Organizing Neural Networks corroborate the practical worth of the logic minimization method for these case studies.
Conclusions
The proposed logic minimization algorithm provides sets of rules that can be used to predict TFBS and O-glycosylation sites with sensitivity and positive predictive value comparable to those from ANN and SVM. Moreover, the logic minimization method has the additional capability of generating interpretable rules that allow biological scientists to correlate the predictions with other experimental results and to form new hypotheses for further investigation. Additional experiments with alternative rule-extraction techniques demonstrate that the logic minimization method is able to produce accurate rules from datasets with large numbers of variables and limited numbers of positive examples.
Thu, 16 Aug 2012 00:00:00 GMThttp://hdl.handle.net/1903/133882012-08-16T00:00:00ZExternalizing behavior in early childhood and body mass index from age 2 to 12 years: longitudinal analyses of a prospective cohort studyhttp://hdl.handle.net/1903/13368
Externalizing behavior in early childhood and body mass index from age 2 to 12 years: longitudinal analyses of a prospective cohort study
Anderson, Sarah E; He, Xin; Schoppe-Sullivan, Sarah; Must, Aviva
Background: Some evidence suggests that obesity and behavior problems are related in children, but studies have
been conflicting and have rarely included children under age 4. An association between behavior problems in early
childhood and risk for obesity could suggest that a common set of factors contribute to both. Our research objectives
were to determine the extent to which externalizing behavior in early childhood is related to body mass index (BMI) in
early childhood and through age 12, and to evaluate whether these associations differ by sex and race.
Methods: Data from the NICHD Study of Early Child Care and Youth Development were analyzed. Externalizing
behaviors at 24 months were assessed by mothers using the Child Behavior Checklist. BMI was calculated from
measured height and weight assessed 7 times between age 2 and 12 years. Linear mixed effects models were used to
assess associations between 24 month externalizing behavior and BMI from 2 to 12 years, calculate predicted
differences in BMI, and evaluate effect modification.
Results: Externalizing behavior at 24 months was associated with a higher BMI at 24 months and through age 12.
Results from a linear mixed effects model, controlling for confounding variables and internalizing behavior, predicted a
difference in BMI of approximately 3/4 of a unit at 24 months of age comparing children with high levels of
externalizing behavior to children with low levels of externalizing behavior. There was some evidence of effect
modification by race; among white children, the average BMI difference remained stable through age 12, but it
doubled to 1.5 BMI units among children who were black or another race.
Conclusions: Our analyses suggest that externalizing behaviors in early childhood are associated with children's
weight status early in childhood and throughout the elementary school years, though the magnitude of the effect is
modest.
Wed, 14 Jul 2010 00:00:00 GMThttp://hdl.handle.net/1903/133682010-07-14T00:00:00ZEmergency Preparedness: Knowledge and Perceptions of Latin American Immigrantshttp://hdl.handle.net/1903/7554
Emergency Preparedness: Knowledge and Perceptions of Latin American Immigrants
Carter-Pokras, Olivia; Zambrana, Ruth E.; Mora, Sonia E.; Aaby, Katherine A.
This paper describes the level of public emergency knowledge and perceptions of
risks among Latin American immigrants, and their preferred and actual sources of emergency
preparedness information (including warning signals). Five Latino community member focus
groups, and one focus group of community health workers, were conducted in a suburban
county of Washington D.C. (N51). Participants came from 13 Latin American countries,
and 64.7% immigrated during the previous five years. Participants had difficulty defining
emergency and reported a wide range of perceived personal emergency risks: immigration
problems; crime, personal insecurity, gangs; home/traffic accidents; home fires; environmental
problems; and snipers. As in previous studies, few participants had received information
on emergency preparedness, and most did not have an emergency plan. Findings regarding
key messages and motivating factors can be used to develop clear, prioritized messages for
communication regarding emergencies and emergency preparedness for Latin American
immigrant communities in the U.S.
Fri, 01 Jan 1999 00:00:00 GMThttp://hdl.handle.net/1903/75541999-01-01T00:00:00ZAssessing Health Concerns and Barriers in a Heterogeneous Latino Communityhttp://hdl.handle.net/1903/7553
Assessing Health Concerns and Barriers in a Heterogeneous Latino Community
Martinez, Iveris L.; Carter-Pokras, Olivia
Introduction. Major health issues and barriers to health services for Latino immigrants
were identified through community-based participatory research in Baltimore city.
Methods. In collaboration with community partners, five focus groups were conducted
among Latino adults from 10 countries and health service providers. Findings. Priorities
across groups included chronic diseases, HIV/AIDS and STDs, mental health, and the need
for ancillary services. Community members and providers did not always agree on what
health matters were of primary concern. Participants expected to receive health information
at the point of service. Barriers to receiving health services and information span linguistic,
financial, logistical, legal, and cultural matters. Conclusions. This formative research
illustrates the complexity and interrelatedness of health priorities and barriers created by
social issues such as employment, legal status, and related stressors.
Sun, 01 Jan 2006 00:00:00 GMThttp://hdl.handle.net/1903/75532006-01-01T00:00:00Z